Novel fluorescent dyes based on oligopropylamines for the in vivo staining of eukaryotic unicellular algae

A review on diatom biosilicification and their adaptive ability to uptake other metals into their frustules for potential application in bone repair

Diatoms are unicellular eukaryotic algae that have a distinctive siliceous cell wall (frustule) with unique architectures. The nanotopography of the frustule is perfectly replicated between generations, offering a source of highly intricate and identical silica microparticles. In recent years, the ability to alter their cell wall chemistry both in terms of functionalisation with organic moieties or by incorporation of the metal ions in their frustules has increased interest in their utility for catalysis technologies, and semiconductor and biomedical applications. Herein we review the fundamental biological mechanisms in which diatoms produce their frustule and their ability to substitute different metal ions in their frustule fabrication process. The review focuses on the potential of diatom frustules as a naturally derived biomaterial in bone tissue engineering applications and how their cell walls, comprising biogenic silica, could either partially or fully incorporate other bone therapeutic metal ions, e.g., titanium or calcium, into their frustule. The use of diatom frustules in bone repair also potentially offers a 'greener', more environmentally friendly, biomaterial as they can naturally synthesise oxides of silicon and other metals into their frustules under ambient conditions at a relatively neutral pH. This process would negate the use of harsh organic chemicals and high-temperature processing conditions, often used in the fabrication of silica based biomaterials, e.g., bioactive glass.

Nitric Oxide Photoreleasers with Fluorescent Reporting

Nitric oxide (NO) plays a multifaceted role in human physiology and pathophysiology, and its controlled delivery has great prospects in therapeutic applications. The light-activated uncaging of NO from NO caging compounds allows this free radical to be released with accurate control of site and dosage, which strictly determine its biological effects. Molecular constructs able to activate fluorescence concomitantly to NO release offer the important advantage of easy and real-time tracking of the amount of NO uncaged in a non-invasive fashion even in the cell environment. This contribution provides an overview of the advances in photoactivatable NO releasers bearing fluorescent reporting functionalities achieved in our and other laboratories, highlighting the rationale design and their potential therapeutic applications.

The Probable Mechanism for Silicon Capture by Diatom Algae: Assimilation of Polycarbonic Acids with Diatoms-Is Endocytosis a Key Stage in Building of Siliceous Frustules?

Many organisms including unicellular (diatoms, radiolaria, and chrysophytes), higher plants (rice and horsetail) and animals (sponges) use silica as a main part of skeletons. The bioavailable form of silicon is silicic acid and the mechanism of silicic acid penetration into living cells is still an enigma. Macropinocytosis was assumed as a key stage of the silicon capture by diatoms but assimilation of monomeric silicic acid by this way requires enormous amounts of water to be passed through the cell. We hypothesized that silicon can be captured by diatoms via endocytosis in the form of partially condensed silicic acid (oligosilicates) whose formation on the diatom surface was supposed. Oligosilicates are negatively charged nanoparticles and similar to coils of poly(acrylic acid) (PAA). We have synthesized fluorescent tagged PAA as well as several neutral and positively charged polymers. Cultivation of the diatom Ulnaria ferefusiformis in the presence of these polymers showed that only PAA is able to penetrate into siliceous frustules. The presence of PAA in the frustules was confirmed with chromatography and PAA causes various aberrations of the valve morphology. Growth of U. ferefusiformis and two other diatoms in the presence of tri- and tetracarbonic fluorescent tagged acids points to the ability of diatoms to recognize substances that bear four acidic groups and to include them into siliceous frustules. Thus, partial condensation of silicic acid is a plausible first stage of silicon assimilation.

Multiple Routes to Smart Nanostructured Materials from Diatom Microalgae: A Chemical Perspective

Diatoms are unicellular photosynthetic microalgae, ubiquitously diffused in both marine and freshwater environments, which exist worldwide with more than 100 000 species, each with different morphologies and dimensions, but typically ranging from 10 to 200 µm. A special feature of diatoms is their production of siliceous micro- to nanoporous cell walls, the frustules, whose hierarchical organization of silica layers produces extraordinarily intricate pore patterns. Due to the high surface area, mechanical resistance, unique optical features, and biocompatibility, a number of applications of diatom frustules have been investigated in photonics, sensing, optoelectronics, biomedicine, and energy conversion and storage. Current progress in diatom-based nanotechnology relies primarily on the availability of various strategies to isolate frustules, retaining their morphological features, and modify their chemical composition for applications that are not restricted to those of the bare biosilica produced by diatoms. Chemical or biological methods that decorate, integrate, convert, or mimic diatoms' biosilica shells while preserving their structural features represent powerful tools in developing scalable, low-cost routes to a wide variety of nanostructured smart materials. Here, the different approaches to chemical modification as the basis for the description of applications relating to the different materials thus obtained are presented.

Fluorescently-tagged polyamines for the staining of siliceous materials

Siliceous frustules of diatom algae contain unique long-chain polyamines, including those having more than six nitrogen atoms. These polyamines participate in the formation of the siliceous frustules of the diatoms but their precise physiological role is not clear. The main hypotheses include formation of a polyamine and polyphosphate supramolecular matrix. We have synthesized novel fluorescent dyes from a synthetic oligomeric mixture of polyamines and the fluorophore 7-nitro-2,1,3-benzoxadiazole. The long polyamine chain ensures the high affinity of these dyes to silica, which allows their application in the staining of siliceous materials, such as valves of diatom algae and fossilized samples from sediments. The fluorescently stained diatom valves were found to be promising liquid flow tracers in hydrodynamic tests. Furthermore, complexation of the polyamine component of the dyes with carbonic polymeric acids results in changes to the visible spectrum of the fluorophore, which allows study of the stability of the complex vs the length of the polyamine chain. Using poly (vinyl phosphonic acid) as a model for phosphate functionality in silaffins (a potential matrix in the formation of biogenic silica) little complexation with the polyamine fluorophores was observed, bringing into question the role of a polyamine - polymeric phosphate matrix in biosilicification.

Simultaneous uptake of a Förster transfer dye pair by diatoms: Application in determination of staining density

The simultaneous uptake of PDMPO and Rhodamine B as two fluorescent dyes forming a Förster transfer pair by the diatom Cyclotella meneghiniana is demonstrated by in vivo-fluorochromation. The incorporation density in the cell walls was high enough for achieving resonant energy transfer between the two dyes as detected by fluorescence and excitation spectroscopy. The mean fluorescence lifetime of the donor is shortened in the presence of the acceptor by a factor of 0.75. By determining the mean lifetime from the fluorescence decay fitted by three eponentials, the efficiency of the energy transfer and the acceptor concentration is calculated assuming a homogenous distribution. For an initial concentration of both dyes of 5μM in the culture medium which is at the saturation limit of incorporation, an acceptor incorporation density of 0.6mM is obtained. In addition to such quantitative determinations, efficient emitting systems based on resonant energy transfer between two laser dyes may be useful in photonic applications of the hybrid biomineral. By achieving stimulated emission, the presence of optical modes in diatom frustules, which may act as photonic resonators due to the refractive index contrast to the environment in combination with the more or less regular pore pattern, may be characterized further.

Quantifying diatom silicification with the fluorescent dye, PDMPO

Diatoms require silicic acid to construct ornately detailed cell walls called frustules. The growth and geographic distribution of diatoms is often controlled by the availability of silicic acid. Analytical methods exist to assess diatom community biogenic silica (bSiO2) production, but partitioning production among taxa has been largely qualitative. We present a method for the quantitative analysis of taxa-specific silica production through labeling diatoms with the fluorescent dye PDMPO [2-(4-pyridyl)-5-((4-(2-dimethylaminoethylaminocarbamoyl)methoxy)phenyl)oxazole]. To make PDMPO a quantitative tool: diatom frustules were solubilized to assess the total diatom community incorporation by quantitation of PDMPO fluorescence using a fluorometer, and laser confocal microscopy was used to quantify the fluorescence of PDMPO in single diatom cells. We created a fluorescence standard to intercalibrate the raw fluorescence signals of the fluorometer and microscope and to determine the fluorescence per mole of PDMPO. PDMPO incorporation was converted to silica production using diatom bSiO2:PDMPO incorporation ratios which varied systematically with silicic acid concentration. Above 3 μM Si(OH)4, bSiO2:PDMPO was constant and PDMPO incorporation was converted to silica production using a mole ratio of 2,916 as determined from cultures. Below 3 μM, the ratio was a linear function of [Si(OH)4] (bSiO2:PDMPO = 912.6 × [Si(OH)4]), as determined using data from two oceanographic cruises. Field evaluation of the method showed that total community PDMPO incorporation generally agreed to within 30% of radioisotope-determined silica production. This PDMPO method has the potential to be a powerful tool for understanding physiology, silicification and resource competition among diatom taxa.

Early warning tools for ecotoxicity assessment based on Phaeodactylum tricornutum

Phaeodactylum tricornutum was exposed to various toxic substances (zinc, copper or dodecylbenzenesulfonic acid sodium salt) in accordance with the AlgalToxkit(®) protocol based on the UNI EN ISO 10253 method in order to quantitatively compare the responses obtained by traditional growth-rate inhibition tests with morphological (biovolume) and physiological (chlorophyll-a, phaeophytin ratio) endpoints. A novel approach is proposed for detecting early and sub-lethal effects based on biovolume quantification using confocal microscopy coupled with an image analysis system. The results showed that effects on both biovolume and the photosynthetic complex are sensitive and powerful early warning tools for evaluating sub-lethal effects of exposure. Specifically, biovolume showed significant sensitive and early responses for the tested surfactant. Qualitatively, we also observed structural anomalies and effects on natural auto-fluorescence in exposed cells that also represent potentially useful tools for ecotoxicological studies.

Fluorescent silk cocoon creating fluorescent diatom using a "Water glass-fluorophore ferry"

Fluorophores are ubiquitous in nature. Naturally occurring fluorophores are exceptionally stable and have high quantum yield. Several natural systems have acquired fluorescent signature due to the presence of these fluorophores. Systematic attempt to harvest these fluorophores from natural systems could reap rich commercial benefit to bio-imaging industry. Silk cocoon biomaterial is one such example of natural system, which has acquired a fluorescent signature. The objective of this study is to develop simple, rapid, commercially viable technique to isolate silk cocoon membrane fluorophores and exploring the possibility of using them as fluorescent dye in bio-imaging. Here, we report an innovative water glass (Na2SiO3) based strategy to isolate the silk cocoon fluorophores. Isolated fluorophore is majorly quercetin derivatives and exhibited remarkable photo- and heat stability. Fluorescence and mass spectrometric analysis confirmed presence of a quercetin derivative. We further used this fluorophore to successfully label the silicate shell of diatom species Nitzschia palea.

Putative silicon transport vesicles in the cytoplasm of the diatom Synedra acus during surge uptake of silicon

We studied the growth of the araphid pennate diatom Synedra acus subsp. radians (Kützing) Skabichevskii using a fluorescent dye N(1),N(3)-dimethyl-N(1)-(7-nitro-2,1,3-benzoxadiazol-4-yl)propane-1,3-diamine (NBD-N2), which stains growing siliceous frustules but does not stain other subcellular organelles. We used a clonal culture of S. acus that was synchronized by silicon starvation. Epifluorescence microscopy was performed in two different ways with cells stained by the addition of silicic acid and the dye. Individual cells immobilized on glass were observed during the first 15-20 min following the replenishment of silicic acid after silicon starvation. Alternatively, we examined cells of a batch culture at time intervals during 36 h after the replenishment of silicic acid using fluorescence and confocal microscopy. The addition of silicic acid and NBD-N2 resulted in the rapid (1-2 min) formation of several dozen green fluorescent submicrometer particles (GFSPs) in the cytoplasm, which was accompanied by the accumulation of fluorescent silica inside silica deposition vesicles (SDVs) along their full length. In 5-15 min, GFSPs disappeared from the cytoplasm. Mature siliceous valves were formed within the SDVs during the subsequent 14-16 h. In the next 8-10 h, GFSPs appeared again in the cytoplasm of daughter cells. The data obtained confirm observations about the two-stage mechanism of silicon assimilation, which includes rapid silicon uptake (surge uptake) followed by slow silica deposition. It is likely that the observed GFSPs are silicon transport vesicles, which were first proposed by Schmid and Schulz in (Protoplasma 100:267-288, 1979).

Dissection of the frustules of the diatom Synedra acus under the action of picosecond impulses of submillimeter laser irradiation

Diatom algae realize highly intriguing processes of biosynthesis of siliceous structures in living cells under moderate conditions. Investigation of diatom physiology is complicated by frustule (siliceous exoskeleton). Frustules consist of valves and girdle bands which are adhered to each other by means of organic substances. Removal of the frustule from the lipid membrane of diatom cells would open new possibilities for study of silicon metabolism in diatoms. We found that submillimeter laser irradiation produced by a free-electron laser causes splitting of diatom frustules without destruction of cell content. This finding opens the way to direct study of diatom cell membrane and to isolation of cell organelles, including silica deposition vesicles. We suppose that the dissection action of the submillimeter irradiation results from unusual ultrasonic waves produced by the short (30-100 ps) but high-power (1 MW) terahertz laser impulses at 5.6 MHz frequency.

An overview of the fundamentals of the chemistry of silica with relevance to biosilicification and technological advances

Biomineral formation is widespread in nature, and occurs in bacteria, single-celled protists, plants, invertebrates, and vertebrates. Minerals formed in the biological environment often show unusual physical properties (e.g. strength, degree of hydration) and often have structures that exhibit order on many length scales. Biosilica, found in single-celled organisms through to higher plants and primitive animals (sponges), is formed from an environment that is undersaturated with respect to silicon, and under conditions of approximately neutral pH and relatively low temperatures of 4-40 °C compared to those used industrially. Formation of the mineral may occur intracellularly or extracellularly, and specific biochemical locations for mineral deposition that include lipids, proteins and carbohydrates are known. In most cases, the formation of the mineral phase is linked to cellular processes, an understanding of which could lead to the design of new materials for biomedical, optical and other applications. In this contribution, we describe the aqueous chemistry of silica, from uncondensed monomers through to colloidal particles and 3D structures, that is relevant to the environment from which the biomineral forms. We then describe the chemistry of silica formation from alkoxides such as tetraethoxysilane, as this and other silanes have been used to study the chemistry of silica formation using silicatein, and such precursors are often used in the preparation of silicas for technological applications. The focus of this article is on the methods, experimental and computational, by which the process of silica formation can be studied, with an emphasis on speciation.

Fluorescent labeling of proteins with amine-specific 1,3,2-(2H)-dioxaborine polymethine dye

A novel water-soluble amine-reactive dioxaborine trimethine dye was synthesized in a good yield and characterized. The potential of the dye as a specific reagent for protein labeling was demonstrated with bovine serum albumin and lysozyme. Its interaction with proteins was studied by fluorescence spectroscopy and gel electrophoresis. The covalent binding of this almost nonfluorescent dye to proteins results in a 75- to 78-fold increase of its emission intensity accompanied by a red shift of the fluorescence emission maximum by 27 to 45 nm, with fluorescence wavelengths of labeled biomolecules being more than 600 nm. The dye does not require activation for the labeling reaction and can be used in a variety of bioassay applications.

Staining diatoms with rhodamine dyes: control of emission colour in photonic biocomposites

The incorporation of rhodamine dyes in the cell wall of diatoms Coscinodiscus granii and Coscinodiscus wailesii for the production of luminescent hybrid nanostructures is investigated. By systematic variation of the substitution pattern of the rhodamine core, we found that carbonic acids are considerably better suited than esters because of their physiological compatibility. The amino substitution pattern that controls the optical properties of the chromophore has no critical influence on dye uptake and incorporation, thus a variety of biocomposites with different emission maxima can be prepared. Applications in biomineralization studies as well as in materials science are envisioned.